Try using

   run("Make Substack...", "slices=3");

if the image is not multi-channel composite color or a hyperstack.

Dear Wayne,

Thank you very much for your suggestion. My images have 3 channels and 10 slices. I really just want to obtain the 10 slices of channel 3.

In addition to not being able to make substacks, I had problems with Z-projections and duplicating images, all having to do with managing hyper stacks. This is both from within proven macros and directly from the menu.

I have come to think that the problem might have arisen after I updated both FiJi and Java on Friday. Everything worked perfectly well before both updates. I do not know which one is the culprit, I lean towards a miscommunication between Java and FiJi, but I'm not sure.

I started using ImageJ also updated to 1.49p and I only added updated versions of LOCI import/export tools and the "Find focused slices" plugin. All works well in ImageJ but not in FiJi.

Again, thank you so very much for looking into this bug.

All best,
Andrés

I am unable to duplicate this problem. When I use the File>New>Hyperstack command to create a 3 channel, 10 slice hyperstack and run

   run("Make Substack...", "channels=3");

I get a 1 channel, 10 slice stack. I also tried z-projecting and duplicating the Organ of Corti sample hyperstack and both commands worked as expected.

I get the following exception if I use

   run("Make Substack...", "channels=3")

on a 3 channel, 10 slice hyperstack with "Enable ImageJ2 data structures" checked in Edit>Options>ImageJ2.

(Fiji Is Just) ImageJ 2.0.0-rc-25/1.49p; Java 1.8.0_25 [64-bit]; Mac OS X 10.10.1; 92MB of 6983MB (1%)
 
java.lang.NullPointerException
	at net.imagej.legacy.translate.AbstractDisplayCreator.getDataset(AbstractDisplayCreator.java:76)
	at net.imagej.legacy.translate.GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
	at net.imagej.legacy.translate.GrayDisplayCreator.makeDisplay(GrayDisplayCreator.java:129)
	at net.imagej.legacy.translate.AbstractDisplayCreator.createDisplay(AbstractDisplayCreator.java:63)
	at net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:100)
	at net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:84)
	at net.imagej.legacy.LegacyImageMap.registerLegacyImage(LegacyImageMap.java:271)
	at net.imagej.legacy.DefaultLegacyHooks.registerImage(DefaultLegacyHooks.java:177)
	at ij.gui.ImageWindow.show(ImageWindow.java)
	at ij.gui.ImageWindow.<init>(ImageWindow.java:138)
	at ij.gui.StackWindow.<init>(StackWindow.java:28)
	at ij.gui.StackWindow.<init>(StackWindow.java:24)
	at ij.ImagePlus.show(ImagePlus.java:418)
	at ij.ImagePlus.show(ImagePlus.java:393)
	at ij.plugin.SubHyperstackMaker.run(SubHyperstackMaker.java:54)
	at ij.plugin.SubstackMaker.run(SubstackMaker.java:33)
	at ij.IJ.runPlugIn(IJ.java:169)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:61)
	at ij.IJ.run(IJ.java:275)
	at ij.macro.Functions.doRun(Functions.java:591)
	at ij.macro.Functions.doFunction(Functions.java:89)
	at ij.macro.Interpreter.doStatement(Interpreter.java:226)
	at ij.macro.Interpreter.doStatements(Interpreter.java:214)
	at ij.macro.Interpreter.run(Interpreter.java:111)
	at ij.macro.Interpreter.run(Interpreter.java:81)
	at ij.macro.Interpreter.run(Interpreter.java:92)
	at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
	at ij.IJ.runMacro(IJ.java:116)
	at ij.IJ.runMacro(IJ.java:105)
	at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:794)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
	at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:160)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

Duplicate of #1010. Fixed and uploaded. Run Help > Update... to receive the fix.

Note that it is also recommended to disable the "Enable ImageJ2 data structures" option in Edit > Options > ImageJ2, since this feature is still buggy and causes performance problems.

Dear Wayne and Curtis,

Thank you so very much for troubleshooting this bug. I had forgotten to add that I had enabled ImageJ2. I updated FiJi and disabled ImageJ2 data structures. Together, this solved my problems.

Again, thank you very much for your help.

Cheers,
Andrés